[gmx-users] number of water molecules affects the PMF

XAvier Periole x.periole at rug.nl
Wed Jun 2 09:58:04 CEST 2010

On Jun 2, 2010, at 9:49 AM, Ozge Engin wrote:

> Hi Chris,
> The two setups were different from each other in terms of only the  
> number of water molecules. Even the starting
> conformations for the two peptides were the same. I especially took  
> care about that to leave only the number of molecules as a variable.
> I calculated the error by dividing the whole data to 4, and  
> calculated the standard deviation between the 4 sets, and divided  
> the result by sqrt (3).
> For the Xavier's suggestion: I think I should wait a little, at  
> least until having the same length of trajectory for the two sets.
Here we go! You are probably not converged! How long did you simulate?
> Thanks
> -- 
> Ozge Engin
> ★☆
> -- 
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before  
> posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

More information about the gromacs.org_gmx-users mailing list